D&D LE loading two balls in the shooter lane?

All of a sudden my D&D LE is loading two balls in the shooter lane and I can't figure out why. It started doing it after a Dragon Multiball and the machine started doing a ball search. It was perpetually searching as if a ball was missing somewhere. I turned the machine off and ejected all 8 balls and put them back in. When I turned it on, it began a ball search again until I noticed the balls were not rolling to the end of the trough. I gave a little push with my finger to get them all the way into the trough and it then loaded two balls into the lane. I pulled one out and dropped it into the drain and it acted like nothing happened. I then dropped the second ball into the drain and it registered. It then once again loaded two ball into the shooter lane. Does anyone have any input on what is happened with this and how to fix it?